Protein-protein interaction as a predictor of subcellular location

Chang Jin Shin, Simon Wong, Melissa J. Davis and Mark A. Ragan

Overview
These are the datasets that were used for the analysis of PPI as a SCL predictor in .Protein-protein interaction as a predictor of subcellular location. (Shin et al, BMC Systems Biology, 2009). The information is presented as tab-delimited files similar to psimitab format and Perl scripts. Brief column descriptions are given for each set and details described in the README file.

Files

Integrated PPI dataset

-Description: PPI dataset for four species were collected from publicly available PPI databases.

-Column descriptions: interactor_A, interactor_B, DB, PMID, PSI_MI, Description

PPI-human-Shin et al-2009.tab
PPI-mouse-Shin et al-2009.tab
PPI-fly-Shin et al-2009.tab
PPI-yeast-Shin et al-2009.tab
PPI-README.txt

Predicted SCL of unknown proteins

-Description: These files describe predicted SCLs of unknown proteins, where one of the interacting partners is known and the other is unknown by using three variants (MERGED, COMMON and MARJORITY) of our approach. The existence of PPIs in subsets also is described.

-Column descriptions: interactor_A, interactor_B, Orig DB(s). interaction, Alt. ID(s), Alt. ID(s), GO(s). interactor_A, GO(s). interactor_B, Subset. Ref, Subset. BP, Subset. DDI, Subset. Interolog, Subset. PMID, Subset. Method, Subset. DB, Union. BIO, Union. EVI, Union. ALL, MERGED_A, MERGED_B, COMMON_A, COMMON_B, MAJORITY_A, MAJORITY_B

SCL-human-Shin et al-2009.tab
SCL-mouse-Shin et al-2009.tab
SCL-fly-Shin et al-2009.tab
SCL-yeast-Shin et al-2009.tab
SCL-README.txt

Scripts for three variants (MERGED, COMMON and MAJORITY)

-Description: Three perl scripts for the three variants of our prediction methods.

Variants.zip

Contact

Contact to c.shin@imb.uq.edu.au OR m.ragan@imb.uq.edu.au